Extended Evaluation of Viral Diversity in Lake Baikal through Metagenomics.
Ontology highlight
ABSTRACT:
SUBMITTER: Butina TV
PROVIDER: S-EPMC8066274 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:BackgroundLake Baikal is the largest body of liquid freshwater on Earth. Previous studies have described the microbial composition of this habitat, but the viral communities from this ecosystem have not been characterized in detail.ResultsHere, we describe the viral diversity of this habitat across depth and seasonal gradients. We discovered 19,475 bona fide viral sequences, which are derived from viruses predicted to infect abundant and ecologically important taxa that reside in Lake Baikal, such as Nitrospirota, Methylophilaceae, and Crenarchaeota. Diversity analysis revealed significant changes in viral community composition between epipelagic and bathypelagic zones. Analysis of the gene content of individual viral populations allowed us to describe one of the first bacteriophages that infect Nitrospirota, and their extensive repertoire of auxiliary metabolic genes that might enhance carbon fixation through the reductive TCA cycle. We also described bacteriophages of methylotrophic bacteria with the potential to enhance methanol oxidation and the S-adenosyl-L-methionine cycle.ConclusionsThese findings unraveled new ways by which viruses influence the carbon cycle in freshwater ecosystems, namely, by using auxiliary metabolic genes that act upon metabolisms of dark carbon fixation and methylotrophy. Therefore, our results shed light on the processes through which viruses can impact biogeochemical cycles of major ecological relevance. Video Abstract.
| S-EPMC7678222 | biostudies-literature
Project description:Viruses are the most abundant and diverse genetic entities on Earth; however, broad surveys of viral diversity are hindered by the lack of a universal assay for viruses and the inability to sample a sufficient number of individual hosts. This study utilized vector-enabled metagenomics (VEM) to provide a snapshot of the diversity of DNA viruses present in three mosquito samples from San Diego, California. The majority of the sequences were novel, suggesting that the viral community in mosquitoes, as well as the animal and plant hosts they feed on, is highly diverse and largely uncharacterized. Each mosquito sample contained a distinct viral community. The mosquito viromes contained sequences related to a broad range of animal, plant, insect and bacterial viruses. Animal viruses identified included anelloviruses, circoviruses, herpesviruses, poxviruses, and papillomaviruses, which mosquitoes may have obtained from vertebrate hosts during blood feeding. Notably, sequences related to human papillomaviruses were identified in one of the mosquito samples. Sequences similar to plant viruses were identified in all mosquito viromes, which were potentially acquired through feeding on plant nectar. Numerous bacteriophages and insect viruses were also detected, including a novel densovirus likely infecting Culex erythrothorax. Through sampling insect vectors, VEM enables broad survey of viral diversity and has significantly increased our knowledge of the DNA viruses present in mosquitoes.
| S-EPMC3108952 | biostudies-literature
Project description:BackgroundVision is a crucial sense for the evolutionary success of many animal groups. Here we explore the diversity of visual pigments (opsins) in the transcriptomes of amphipods (Crustacea: Amphipoda) and conclude that it is restricted to middle (MWS) and long wavelength-sensitive (LWS) opsins in the overwhelming majority of examined species.ResultsWe evidenced (i) parallel loss of MWS opsin expression in multiple species (including two independently evolved lineages from the deep and ancient Lake Baikal) and (ii) LWS opsin amplification (up to five transcripts) in both Baikal lineages. The number of LWS opsins negatively correlated with habitat depth in Baikal amphipods. Some LWS opsins in Baikal amphipods contained MWS-like substitutions, suggesting that they might have undergone spectral tuning.ConclusionsThis repeating two-step evolutionary scenario suggests common triggers, possibly the lack of light during the periods when Baikal was permanently covered with thick ice and its subsequent melting. Overall, this observation demonstrates the possibility of revealing climate history by following the evolutionary changes in protein families.
| S-EPMC8108468 | biostudies-literature
Project description:Transitions between saline and fresh waters have been shown to be infrequent for microorganisms. Based on host-specific interactions, the presence of specific clades among hosts suggests the existence of freshwater-specific viral clades. Yet, little is known about the composition and diversity of the temperate freshwater viral communities, and even if freshwater lakes and marine waters harbor distinct clades for particular viral sub-families, this distinction remains to be demonstrated on a community scale.To help identify the characteristics and potential specificities of freshwater viral communities, such communities from two lakes differing by their ecological parameters were studied through metagenomics. Both the cluster richness and the species richness of the Lake Bourget virome were significantly higher that those of the Lake Pavin, highlighting a trend similar to the one observed for microorganisms (i.e. the specie richness observed in mesotrophic lakes is greater than the one observed in oligotrophic lakes). Using 29 previously published viromes, the cluster richness was shown to vary between different environment types and appeared significantly higher in marine ecosystems than in other biomes. Furthermore, significant genetic similarity between viral communities of related environments was highlighted as freshwater, marine and hypersaline environments were separated from each other despite the vast geographical distances between sample locations within each of these biomes. An automated phylogeny procedure was then applied to marker genes of the major families of single-stranded (Microviridae, Circoviridae, Nanoviridae) and double-stranded (Caudovirales) DNA viruses. These phylogenetic analyses all spotlighted a very broad diversity and previously unknown clades undetectable by PCR analysis, clades that gathered sequences from the two lakes. Thus, the two freshwater viromes appear closely related, despite the significant ecological differences between the two lakes. Furthermore, freshwater viral communities appear genetically distinct from other aquatic ecosystems, demonstrating the specificity of freshwater viruses at a community scale for the first time.
| S-EPMC3303852 | biostudies-literature
Project description:Uncoupling between molecular and morphological evolution is common in many animal and plant lineages. This is especially frequent among groups living in ancient deep lakes, because these ecosystems promote rapid morphological diversification, and has already been demonstrated for Tanganyika cychlid fishes and Baikal amphipods. Ostracods are also very diverse in these ecosystems, with 107 candonid species described so far from Baikal, majority of them in the genera Candona Baird, 1845 and Pseudocandona Kaufmann, 1900. Here we study their morphological and molecular diversity based on four genes (two nuclear and two mitochondrial), 10 species from the lake, and 28 other species from around the world. The results of our phylogenetic analysis based on a concatenated data set, along with sequence diversity, support only two genetic lineages in the lake and indicate that a majority of the Baikal Candona and Pseudocandona species should be excluded from these genera. We describe a new genus, Mazepovacandonagen. n., to include five Baikal species, all redescribed here. We also amend the diagnosis for the endemic genus Baicalocandona Mazepova, 1972 and redescribe two species. Our study confirms an exceptional morphological diversity of Lake Baikal candonids and shows that both Baikal lineages are closely related to Candona, but only distantly to Pseudocandona.
| S-EPMC5523182 | biostudies-literature
Project description:In this paper, the very first checklist of the freshwater leeches of Maloe More Strait, a special part of Lake Baikal, is presented. It includes 14 free-living and parasitic species, of which four species belong to endemic Baikal genera - two species from Baicalobdella and one species each from Baicaloclepsis and Codonobdella. The checklist highlights six potentially new morphological species recorded for the first time in the area. The exact systematic position is stated for all leech species. Each species from the list is provided with information on taxonomic synonymy, data on its geographic distribution, and ecological characteristics. New species records are additionally provided with brief morphological characteristics and photos of their external morphology.
| S-EPMC4714365 | biostudies-literature
Project description:Recent metagenomic sequencing studies of uncultured viral populations have provided novel insights into the ecology of environmental bacteriophage. At the same time, viral metagenomes could also represent a potential source of recombinant proteins with biotechnological value. In order to identify such proteins, a novel two-step screening technique was devised for cloning phage lytic enzymes from uncultured viral DNA. This plasmid-based approach first involves a primary screen in which transformed Escherichia coli clones that demonstrate colony lysis following exposure to inducing agent are identified. This effect, which can be due to the expression of membrane-permeabilizing phage holins, is discerned by the development a hemolytic effect in surrounding blood agar. In a secondary step, the clones identified in the primary screen are overlaid with autoclaved Gram-negative bacteria (specifically Pseudomonas aeruginosa) to assay directly for recombinant expression of lytic enzymes, which are often encoded proximally to holins in phage genomes. As proof-of-principle, the method was applied to a viral metagenomic library constructed from mixed animal feces, and 26 actively expressed lytic enzymes were cloned. These proteins include both Gram-positive-like and Gram-negative-like enzymes, as well as several atypical lysins whose predicted structures are less common among known phage. Overall, this study represents one of the first functional screens of a viral metagenomic population, and it provides a general approach for characterizing lysins from uncultured phage.
| S-EPMC2976241 | biostudies-literature
Project description:BACKGROUND:Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages. RESULTS:We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L-1. The recovered 16S rRNA gene sequences were mostly from Bacteria, even in the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria. CONCLUSIONS:Our first sequencing effort of hypersaline soda lake sediment metagenomes led to two important advances. First, we showed the existence and obtained the first genomes of haloalkaliphilic members of the CPR and several hundred other novel prokaryote lineages. The soda lake CPR is a functionally diverse group, but the most abundant organisms in this study are likely fermenters with a possible role in primary carbon degradation. Second, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducers, and methanogens. Since only few environmental metagenomics studies have targeted sediment microbial communities and never to this extent, we expect that our findings are relevant not only for the understanding of haloalkaline environments but can also be used to set targets for future studies on marine and freshwater sediments.
| S-EPMC6146748 | biostudies-literature
Project description:An aquatic surface microlayer covers more than 70% of the world's surface. Our knowledge about the biology of the surface microlayer of Lake Baikal, the most ancient lake on Earth with a surface area of 31,500 km², is still scarce. The total bacterial abundance, the number of cultured heterotrophic temporal bacteria, and the spatial distribution of bacteria in the surface microlayer and underlying waters of Lake Baikal were studied. For the first time, the chemical composition of the surface microlayer of Lake Baikal was determined. There were significant differences and a direct relationship between the total bacterial abundance in the surface microlayer and underlying waters of Lake Baikal, as well as between the number of cultured heterotrophic bacteria in studied water layers in the period of summer stratification. In the surface microlayer, the share of cultured heterotrophic bacteria was higher than in the underlying waters. The surface microlayer was characterized by enrichment with PO?3-, total organic carbon and suspended particulate matter compared to underlying waters. A direct relationship was found between the number of bacteria in the surface microlayer and environmental factors, including temperature, total organic carbon and suspended particulate matter concentration.
| S-EPMC6266163 | biostudies-literature
Project description:Small lakes have lower water levels during dry years as was the case in 2000-2020. We sought to show the biodiversity of plant communities at various water levels in Lake Arakhley. Changes in moisture content are reflected in the cyclical variations of the water level in the lake, which decreased approximately 2 m in 2017-2018. These variations affect the biological diversity of the aquatic ecosystems. We present the latest data on the state of the plant communities in this mesotrophic lake located in the drainage basin of Lake Baikal. Lake Arakhley is a freshwater lake with low mineral content and a sodium hydrocarbonate chemical composition. Changes in the nutrient concentration were related to precipitation; inflow volume and organic matter were autochtonous at low water levels. The most diverse groups of phytoplankton found in the lake were Bacillariophyta, Chlorophyta, and Chrysophyta. High biodiversity values indicate the complexity and richness of the lake's phytoplankton community. A prevalence of Lindavia comta was observed when water levels were low and Asterionella formosa dominated in high-water years. The maximum growth depth of lacustrine vegetation decreased from 11.0 m to 4.0 m from 1967 to 2018. Decreasing water levels were accompanied by a reduction in the littoral zone, altering the communities of aquatic plants. The hydrophyte communities were monodominant in the dry years and were represented by Ceratophyllum demersum. The vegetation cover of the lake was more diverse in high-water years and variations in the lake's water content altered the composition of biogenic substances. These changes were reflected in the lake's phytocenosis.
| S-EPMC8216174 | biostudies-literature